crossing96/oncoscreening huggingface dataset:
EIF4A3 serves as a prognostic and immunosuppressive microenvironment factor and inhibits cell apoptosis in bladder cancer.	EIF4A3 (Eukaryotic translation initiation factor 4A3 (EIF4A3) was recently recognized as an oncogene; however, its role in BLCA (bladder cancer) remains unclear. We explored EIF4A3 expression and its prognostic value in BLCA in public datasets, including the TCGA (The Cancer Genome Atlas) and GEO (Gene Expression Omnibus). Thereafter, the association between EIF4A3 expression and the infiltration of immune cells and immune-checkpoint expression was determined using TIMER2 (Tumor Immune Estimation Resource 2) tool. Additionally, the impact of EIF4A3 on cellular proliferation and apoptosis events in BLCA cell lines was determined by siRNA technology. In this study, EIF4A3 was found to be significantly upregulated in BLCA, upregulated expression of EIF4A3 was related to poor prognosis, advanced histologic grade, subtype, pathological stage, white race, and poor primary therapy outcome. The immune infiltration analysis revealed that EIF4A3 expression was negatively associated with CD8(+) and CD4(+) T cells and positively with myeloid-derived suppressor cells, macrophage M2, cancer-associated fibroblasts, and Treg cells. Moreover, EIF4A3 was coexpressed with PD-L1 (programmed cell death 1-ligand 1) and its expression was higher in patients responding to anti-PD-L1 therapy. EIF4A3 knockdown significantly inhibited proliferation and promoted apoptosis in 5,637 and T24 cells. In summary, BLCA patients with elevated EIF4A3 expression had an unfavorable prognosis and immunosuppressive microenvironment, and EIF4A3 may facilitate BLCA progression by promoting cell proliferation and inhibiting apoptosis. Furthermore, our study suggests that EIF4A3 is a potential biomarker and therapeutic target for BLCA.	bladder
Current Techniques for En Bloc Transurethral Resection of Bladder Tumor: A Hands-on Guide Through the Energy Landscape.	En bloc resection of bladder tumor (ERBT) has attracted interest as a potentially superior technique to transurethral resection of bladder tumor (TURBT) to obtain detrusor muscle in the specimen. Different ERBT techniques have been described, with bipolar electrocautery and laser being the more favored energy modalities. Electrocautery EBRT has an advantage in terms of widespread availability in clinics and ease of conversion to piecemeal resection in case of large bladder tumors in different locations. Laser EBRT has an advantage in preventing obturator nerve reflex, which is particularly useful for lateral wall tumors. Further research is needed to assess the potential case-related advantages of the ERBT techniques over each other. PATIENT SUMMARY: Surgical removal of a bladder tumor as a whole single piece, called en bloc resection, is a safe procedure for the diagnosis and treatment of noninvasive bladder cancer. In this mini-review we summarize the evidence for current techniques for en bloc resection.	bladder
Development and evaluation of an adenosine-to-inosine RNA editing-based prognostic model for survival prediction of bladder cancer patients.	Adenosine-to-inosine RNA editing (ATIRE) is a common form of ribonucleic acid (RNA) editing, which has highlighted the importance of ATIRE in tumors. However, its role in bladder cancer (BLCA) remains poorly understood. To study ATIRE impact on BLCA patient prognosis, we obtained ATIRE, gene expression, and clinical data from the Cancer Genome Atlas (TCGA) database for 251 patients, randomly dividing them into training and testing groups. Univariate proportional hazards model (COX) regression identified prognosis-associated ATIRE loci, while the least absolute shrinkage and selection operator (LASSO) selected final loci to construct prognostic models and generate ATIRE scores. We developed a nomogram to predict BLCA patients' overall survival (OS) and analyzed the effect of ATIRE editing levels on host gene expression. We also compared immune cell infiltration and drug treatment between patients with high and low ATIRE scores. The ATIRE prognostic prediction model was constructed using ten ATIRE loci that are closely associated with BLCA survival. Patients with high ATIRE scores showed significantly worse OS than those with low ATIRE scores. Furthermore, the nomogram, which incorporates the ATIRE score, can better predict the prognosis of patients. Multiple functional and pathway changes associated with immune responses, as well as significant differences in immune cell infiltration levels and response to drug therapy were observed between patients with high and low ATIRE scores. This study represented the first comprehensive analysis of the role of ATIRE events in BLCA patient prognosis and provided new insights into potential prognostic markers for BLCA research.	bladder
Single-cell RNA sequencing reveals the cellular and molecular characteristics of high-grade and metastatic bladder cancer.	PURPOSE: Metastatic bladder cancer (BC) has the highest somatic mutation frequency and recurrence rate of all tumors. However, the cellular and molecular characteristics of BC remain unclear. METHODS: We performed single-cell RNA sequencing (scRNA-seq) on the samples of paracancerous normal tissue (PNT), primary tumor (PT) and lymph node metastasis (LNM). The proportions and gene expression profiles of different cell types in the tumor microenvironment (TME) were investigated. RESULTS: In total, 50,158 cells were classified into six populations. Malignant cells of PT and LNM exhibited large mutant DNA fragments, while the cell phenotypes and gene expression profiles differed during differentiation. Metastasis was associated with a poorer prognosis than PT. Tumor-associated stromal cells and inhibitory immune cells were the main cell populations in PT and LNM. Cell-cell communication analysis revealed the roles of signaling pathways of inflammatory cancer-associated fibroblast (iCAF) and tumor-associated macrophage (TAM) in exhaustion of T cells. In addition, iCAF may recruit TAM to promote formation of the TME earlier than the differentiation of tumor cells. CONCLUSION: This study through scRNA-seq enhanced our understanding of new features about the cellular and molecular similarities and differences of high-grade and metastatic bladder cancer, which might provide potential therapeutic targets in future treatment.	bladder
Disseminated Bacillus Calmette-Guérin Infection with Rhabdomyolysis, Acute Kidney Injury, and Interstitial Pneumonia after Bacillus Calmette-Guérin Intravesical Instillation Therapy.	A 79-year-old man experienced a fever and immobility after receiving 6 doses of Bacillus Calmette-Guérin (BCG) intravesical instillation therapy for bladder tumor. Rhabdomyolysis and acute kidney injury occurred; therefore, hemodialysis was performed. His kidney function was restored. However, he exhibited an inflammatory reaction that was resistant to broad-spectrum antibiotics and eventually developed interstitial pneumonia. Corticosteroid treatment partially relieved the symptoms of interstitial pneumonia, although disuse syndrome persisted. He was diagnosed with disseminated BCG infection through sputum culture. BCG infection shows various symptoms and is difficult to diagnose microbiologically. It should be suspected when systemic symptoms occur after BCG intravesical instillation therapy.	bladder
Psychosocial distress and quality of life in patients after radical cystectomy - one year follow-up in 842 German patients.	PURPOSE: This study aims to report on psychosocial distress and QoL in bladder cancer patients after radical cystectomy (RC) and urinary diversion to obtain a better basis for patient counseling and postoperative care. METHODS: The study relied on prospectively collected data for 842 patients, who underwent three weeks of inpatient rehabilitation after RC and creation of an ileal conduit (IC) or ileal neobladder (INB). Data on QoL and psychosocial distress were collected by validated questionnaires. Multivariate logistic regression was performed to identify predictors for high psychosocial distress. RESULTS: Four-hundred and forty-seven patients (326 male, 121 female) received an IC, while 395 patients (357 male, 38 female) received an INB. Health-related QoL improved steadily in the whole cohort during follow-up. Patients with an INB reported better physical function but suffered more from diarrhea and financial worries. Patients with an IC reported reduced satisfaction with their body image, increased worries about the future, and suffered more from constipation. Psychosocial distress increased significantly during follow-up. One year after surgery, 43.1% of patients suffered from high psychosocial distress. Multivariate regression analysis identified age ≤ 59 years (OR 1.731; CI 1.056-2.838; p = 0.030) and lymph node metastases (OR 2.073; CI 1.133-3.793; p = 0.018) as independent predictors for high psychosocial distress. CONCLUSION: QoL improves significantly in all patients one year after RC. However, psychosocial distress remains high in a substantial number of patients. IMPLICATIONS FOR CANCER SURVIVORS: To prevent chronic psychological disorders, easily accessible opportunities for psycho-oncological counseling are needed for patients following RC.	bladder
The function of guanylate binding protein 3 (GBP3) in human cancers by pan-cancer bioinformatics.	As a guanylate binding protein (GBPs) member, GBP3 is immune-associated and may participate in oncogenesis and cancer therapy. Since little has been reported on GBP3 in this field, we provide pan-cancer bioinformatics to investigate the role of GBP3 in human cancers. The GBP3 expression, related clinical outcomes, immune infiltrates, potential mechanisms and mutations were conducted using tools including TIMER2.0, GEPIA2.0, SRING, DAVID and cBioPortal. Results showed an increased risk of high GBP3 in Brain Lower Grade Glioma (LGG) and Lung Squamous Cell Carcinoma (LUSC) and a decreased risk of GBP3 in Sarcoma (SARC) and Skin Cutaneous Melanoma (SKCM) (p ≤ 0.05). GBP3 was negatively correlated with CAFs in Esophageal Adenocarcinoma (ESCA) and positively correlated with CAFs in LGG, LUSC and TGCG (p ≤ 0.05). In addition, GBP3 was positively correlated with CD8+ T cells in Bladder Urothelial Carcinoma (BLCA), Cervical Squamous Cell Carcinoma (CESC), Kidney Renal Clear Cell Carcinoma (KIRC), SARC, SKCM, SKCM-Metastasis and Uveal Melanoma (UVM) (p ≤ 0.05). Potentially, GBP3 may participate in the homeostasis between immune and adaptive immunity in cancers. Moreover, the most frequent mutation sites of GBP3 in cancers are R151Q/* and K380N. This study would provide new insight into cancer prognosis and therapy.	bladder
Effect of renin-angiotensin-aldosterone system inhibitors on survival outcomes in cancer patients treated with immune checkpoint inhibitors: a systematic review and meta-analysis.	BACKGROUND: Effect of renin-angiotensin-aldosterone system inhibitors (RAASIs) in combination with immune checkpoint inhibitors (ICIs) on prognoses in cancer patients remains controversial. This study systematically evaluated the effect of RAASIs on survival outcomes in cancer patients receiving ICIs treatment and provided an evidence-based reference for the rational use of RAASIs and ICIs combination therapy in clinical practice. METHODS: Studies evaluating the prognosis of RAASIs-used versus RAASIs-free in cancer patients receiving ICIs treatment from inception to 1 November 2022 were retrieved by searching PubMed, Cochrane Library, Web of Science, Embase, and major conference proceedings. Studies in English reporting hazard ratios (HRs) with 95% confidence intervals (CIs) for overall survival (OS) and/or progression-free survival (PFS) were included. Statistical analyses were conducted using the software Stata 17.0. RESULTS: A total of 12 studies containing 11739 patients were included, comprising ~4861 patients in the RAASIs-used and ICIs-treated group and ~6878 patients in RAASIs-free and ICIs-treated group. The pooled HR was 0.85 (95%CI, 0.75-0.96; P = 0.009) for OS and 0.91 (95%CI, 0.76-1.09; P = 0.296) for PFS, indicating a positive effect of RAASIs concomitant with ICIs on cancer patients. This effect was observed especially in patients with urothelial carcinoma (HR, 0.53; 95%CI, 0.31-0.89; P = 0.018) and renal cell carcinoma (HR, 0.56; 95%CI, 0.37-0.84; P = 0.005) on OS. CONCLUSION: Concomitant use of RAASIs and ICIs enhanced the efficacy of ICIs and this combination regimen was associated with significantly improved OS and a trend towards better PFS. RAASIs can be considered as adjuvant drugs when hypertensive patients receive ICIs treatment. Our results provide an evidence-based reference for the rational use of the RAASIs and ICIs combination therapy to improve the efficacy of ICIs in clinical practice. SYSTEMATIC REVIEW REGISTRATION: https://www.crd.york.ac.uk/prospero/, identifier CRD42022372636; https://inplasy.com/, identifier INPLASY2022110136.	bladder
LDL receptor related protein 1 is an adverse prognostic biomarker that correlates with stromal remodeling and macrophages infiltration in bladder cancer.	INTRODUCTION: Bladder cancer (BLCA) is a highly heterogeneous disease influenced by the tumor microenvironment, which may affect patients' response to immune checkpoint blockade therapy. Therefore, identifying molecular markers and therapeutic targets to improve treatment is essential. In this study, we aimed to investigate the prognostic significance of LRP1 in BLCA. METHODS: We analyzed TCGA and IMvigor210 cohorts to investigate the relationship of LRP1 with BLCA prognosis. We utilized gene mutation analysis and enrichment to identify LRP1-associated mutated genes and biological processes. Deconvolution algorithms and single-cell analysis were used to understand the tumor-infiltrated cells and biological pathways associated with LRP1 expression. Immunohistochemistry was conducted to validate the bioinformatics analysis. RESULTS: Our study revealed that LRP1 was an independent risk factor for overall survival in BLCA patients and was associated with clinicopathological features and FGFR3 mutation frequency. Enrichment analysis demonstrated that LRP1 was involved in extracellular matrix remodeling and tumor metabolic processes. Furthermore, the ssGSEA algorithm revealed that LRP1 was positively correlated with the activities of tumor-associated pathways. Our study also found that high LRP1 expression impaired patients' responsiveness to ICB therapy in BLCA, which was predicted by TIDE prediction and validated by IMvigor210 cohort. Immunohistochemistry confirmed the expression of LRP1 in Cancer-Associated Fibroblasts (CAFs) and macrophages in the tumor microenvironment of BLCA. DISCUSSION: Our study suggests that LRP1 may be a potential prognostic biomarker and therapeutic target in BLCA. Further research on LRP1 may improve BLCA precision medicine and enhance the efficacy of immune checkpoint blockade therapy.	bladder
Identification of a novel de novo mutation of SETBP1 and new findings of SETBP1 in tumorgenesis.	BACKGROUND: In the past decade, SETBP1 has attracted a lot of interest on that the same gene with different type or level (germline or somatic) of variants could provoke different pathologic consequences such as Schinzel-Giedon syndrome, SETBP1 Haploinsufficiency Disorder (SETBP1-HD) and myeloid malignancies. Whole exome sequencing was conducted to detect the etiology of a pregnant woman with mental retardation. As a new oncogene and potential marker of myeloid malignancies, somatic SETBP1 variants in other cancers were rarely studied. We performed a pan-cancer analysis of SETBP1 gene in different cancers for the first time. RESULTS: A novel heterozygous mutation of the SETBP1 gene (c.1724_1727del, p.D575Vfs*4) was found in the patient and the fetus and the mutation was predicted to result in a truncated protein. Reduced SETBP1 expression was associated with SETBP1-HD. The pan-cancer analysis of SETBP1 showed that SETBP1 overexpression should be given special attention in Bladder Urothelial Carcinoma (BLCA) and Stomach adenocarcinoma (STAD). CONCLUSIONS: The de novo SETBP1 mutation was the genetic cause of SETBP1-HD in the family. BLCA and STAD might be related to SETBP1 overexpression.	bladder
Diagnostic accuracy of bimanual palpation in bladder cancer patients undergoing cystectomy: A prospective study.	OBJECTIVES: To prospectively assess the concordance of examination under anesthesia (EUA)-based clinical T stage with pathological T stage and diagnostic accuracy of EUA in patients with bladder cancer undergoing cystectomy. METHODS: Consecutive patients with bladder cancer undergoing cystectomy between June 2017 and October 2020 in a single academic center were included in a prospective study. Two urologists performed EUA (one blinded to imaging) before patients underwent cystectomy. We assessed the concordance between clinical T stage in bimanual palpation (index test) and pathological T stage in cystectomy specimens (reference test). Sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were calculated with 95% confidence intervals (CIs) to detect or exclude locally advanced bladder cancer (pT3b-T4b) in EUA. RESULTS: The data of 134 patients were analyzed. Given that stage pT3a cannot be palpated, for the nonblinded examiner, T staging in EUA was concordant with pT in 107 (79.9%) patients, 20 (14.9%) cases being understaged in EUA and 7 (5.2%) overstaged. For the blinded examiner, staging was correct in 106 (79.1%) patients, 20 (14.9%) cases being understaged and 8 (6%) overstaged. For the nonblinded examiner, sensitivity, specificity, PPV, and NPV of EUA were 55.9% (95% CI 39.2%-72.6%), 93% (88%-98%), 73.1% (56%-90.1%), and 86.1% (79.6%-92.6%), respectively; for the blinded examiner, they were 52.9% (36.2%-69.7%), 93% (88%-98%), 72% (54.4%-89.6%) and 85.3% (78.7%-92%), respectively. Awareness of imaging results did not have a major impact on EUA results. CONCLUSION: Bimanual palpation should still be used for clinical staging, given its specificity, NPV, and that it could correctly determine bladder cancer T stage in 80% of cases.	bladder
Evaluation of short-term outcomes of neoadjuvant chemotherapy followed by radical cystectomy in muscle-invasive bladder cancer: a single Egyptian institution experience.	BACKGROUND AND AIM: Neoadjuvant chemotherapy (NAC) before radical cystectomy (RC) became the standard of care for muscle-invasive bladder cancer (MIBC) in the last few years. We aimed to evaluate the radiological, pathological responses to NAC, and the 30-day surgical outcomes after RC in MIBC. PATIENTS AND METHODS: A retrospective cohort study involving adult patients with localized urothelial MIBC who received NAC followed by RC at the National Cancer Institute of Egypt (NCI-E) for 2 years (2017 and 2018). Out of 235 MIBC cases, we recognized 72 patients (30%) who fitted the eligibility criteria. RESULTS: A cohort of 72 patients with a median age of 60.5 years (range 34-87). Hydronephrosis, gross extravesical extension (cT3b), and radiologically negative nodes (cN0) were depicted initially in 45.8, 52.8, and 83.3% of patients, respectively. Gemcitabine and cisplatin (GC) was the rampant NAC employed in 95.8%. Radiological evaluation post NAC using RECIST v1.1 revealed a response rate (RR) of 65.3% in bladder tumor and progressive disease in the former and lymph nodes encountered in 19.4 and 13.9%, respectively. The median time from the end of NAC to surgery was 8.1 weeks (range 4-15). Open RC and ileal conduit were the most common types of surgery and urinary diversion, respectively. Pathological down-staging was encountered in 31.9%, and only 11 cases (15.3%) achieved pathological complete response (pCR). The latter was significantly correlated with the absence of hydronephrosis, low-risk tumors, and associated bilharziasis (p = 0.001, 0.029, and 0.039, respectively). By logistic regression, the high-risk category was the only independent factor associated with a poor likelihood of achieving pCR (OR 4.3; 95% CI 1.1-16.7; p = 0.038). Thirty-day mortality occurred in 5(7%) patients, and 16(22%) experienced morbidity, with intestinal leakage being the most frequent complication. cT4 was the only significant factor associated with post-RC morbidity and mortality compared to cT2 and cT3b (p = 0.01). CONCLUSIONS: Our results are further supporting the radiological and pathological benefits of NAC in MIBC, evidenced by tumor downstaging and pCR. The complication rate after RC is still considerable; hence, more larger studies are necessary to postulate a comprehensive risk assessment tool for patients who would get the maximum benefit from NAC, hoping to accomplish higher complete response rates with ultimately increased adoption of the bladder preservation strategies.	bladder
Xanthogranulomatous Ureteritis: A Diagnostic Challenge in a Patient with Bladder Cancer.	Xanthogranulomatous ureteritis is a very rare process characterized by the presence of foamy histiocytes in a background of chronic active inflammation affecting the ureteral wall. Herein, we describe a case of a 64-year-old man with bladder cancer affecting the left posterolateral wall of the bladder. Radiologically, there was a suspicion of multifocal involvement of the ureteral wall. The patient underwent a radical cystectomy with bilateral pelvic lymphadenectomy and a laparoscopic left nephroureterectomy. Histopathologic examination of the radical cystectomy revealed an invasive high-grade urothelial carcinoma. The wall of the left ureter was replaced by abundant foamy histocytes and a mixed inflammatory infiltrate with lymphocytes and plasma cells consistent with xanthogranulomatous ureteritis. In this report, we highlight the importance of awareness of this benign process when observing a ureteral mass in cancer patients.	bladder
Pelvic Organ Preservation in Non-muscle-invasive Bladder Cancer: Less Is More.	Radical cystectomy (RC) is a treatment option for high-risk non-muscle-invasive bladder cancer (NMIBC) but is associated with high morbidity and a negative impact on quality of life. Reproductive or pelvic organ-sparing cystectomy (ROSC) techniques have emerged as a potential strategy to mitigate some potential effects of standard RC. Here we discuss current knowledge regarding oncological, functional, and sexual function outcomes associated with ROSC and their applicability in NMIBC. These outcomes can be used to make informed clinical decisions regarding cystectomy technique in appropriately staged and selected patients with NMIBC. PATIENT SUMMARY: We reviewed results for bladder cancer control, urinary function, and sexual function after removal of the bladder with and without techniques to spare reproductive or pelvic organs. We found evidence of better sexual function outcomes with a sparing approach without compromise of cancer control. Further studies are needed to assess urinary function and pelvic floor-related outcomes.	bladder